Abstract The hyporheic zone is an ecotone connecting the stream and groundwater ecosystem that plays a significant role for stream biogeochemistry. Water exchange across the stream-sediment interface and biogeochemical reactions in the streambed concur to affect subsurface solute concentrations and eventually nutrient cycling in the fluvial corridor. In this paper we investigate the interplay of hydrological and biogeochemical processes in a duned streambed and their effect on spatial distribution of solutes. We employ a numerical model to simulate the turbulent water flow and the pressure distribution over the dunes, and then to evaluate the flow field and the biogeochemical reactions in the hyporheic sediments. Sensitivity analyses are performed to analyze the influence of hydrological and chemical properties of the system on solute reaction rates. The results demonstrate the effect of stream velocity and sediment permeability on the chemical zonation. Changing sediment permeability as well as stream velocity directly affects the nutrient supply and the residence times in the streambed, thus controlling the reaction rates under the dune. Stream-water quality is also shown to influence the reactive behavior of the sediments. In particular, the availability of dissolved organic carbon determines whether the streambed acts as a net sink or source of nitrate. This study represents a step towards a better understanding of the complex interactions between hydrodynamical and biogeochemical processes in the hyporheic zone.